The patient, designated as C, was a patient with non-Hodgkin’s B-cell lymphoma and received a positive test for coronavirus in April 2020. The first negative test was received almost a year later — in March 2021. During this time, the woman suffered from serious symptoms several times, including fever and pneumonia.
Scientists followed the evolution of SARS-CoV-2 in the patient’s body using genome-wide sequencing and phylogenetic analysis, which confirmed that the woman had been suffering from the same infection all this time. The virus has undergone 40 mutations in a year, which is much faster than it occurs in the population. SARS-CoV-2 has adapted to the body of one person, improving its ability to survive and reproduce faster. Some mutations affected the S-protein and were similar to those observed in other patients.
Previously, it was believed that mutations in the S-protein are fixed in response to the action of neutralizing antibodies. Still, patient C had no B-lymphocytes, and she had almost no IgG antibodies. In addition, many mutations occurred on proteins that are not located on the surface of the viral envelope. This is because the patient still had T-cell immunity, recognizing any proteins encoded in the virus genome. Thus, SARS-CoV-2 acquired protection that allows the virus to resist only that part of the immunity that the patient has preserved.
The scientists confirmed that the mutations accumulated by the virus allowed it to purposefully evade the presentation of antigens by the alleles of the main histocompatibility complex (HCС) of the patient, making the T-cell immune response ineffective. The HCС presents foreign molecules to T cells for recognition and subsequent destruction of the pathogen. Probably, new strains that are characterized by increased resistance to antibodies could also arise and quickly accumulate mutations in the body of people with a weakened immune system.